It was decided at a commission board meeting last week to drop a requirement for some organisations to show that trustees had been checked.
Organisations affected include those working with vulnerable adults or children. Board members will instead be asked to sign declarations confirming whether checks have been carried out.
The move is expected to save the commission £100,000 a year, expenditure that the regulator deemed to be "disproportionate to the level of risk".
Sarah Atkinson, head of corporate affairs at the commission, said: "The system has got to be targeted on where the highest risk exists."
After the meeting, governance consultant Linda Laurance said: "It is important that trustees are treated as responsible individuals who will act in the best interests of charities. But it is important that the welfare of beneficiaries is paramount. Anyone who wishes to abuse any system will do so."